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Background Although Mycoplasma genitalium is a common cause of sexually transmitted infection diseases (STI), very little information regarding the prevalence of M.genitalium among MSM (men who have sex with men) is available in China.The objective of this study was to determine the prevalence of M.genitalium among MSM in the city of Shenzhen, Guangdong Province, China, and to identify the potential risk factors associated with M.genitalium infection in this area.